About the distance constraint

[jay]

Hi, all. I am trying to use plumed 2 by using 1 CV( difference of coordination number ).

I am familiar with plumed 1 so I usually use UPPER(LOWER)_WALL commands to constraint the maximum/minimum distance of interatomic distance to prevent undesirable reactions. 

In plumed 2, I am trying to use like below: 

distcn1: DISTANCE ATOMS=238,235  
distcn2: DISTANCE ATOMS=235,199

RESTRAINT ARG=distcn1  KAPPA=100 AT=2.1
RESTRAINT ARG=distcn2 KAPPA=100  AT=2.7

in order not to make atoms diffuse away from the reactive sites.

In this case, the "RESTRAINT" command is proper?  I tried to use UPPER_WALLS ARG=distcn1.max AT=2.14 KAPPA=100 but it seems like not working well.

Thanks in advance. 

[Robert Coffman]

Jay,

Using the RESTRAINT command you are making a harmonic restraint to keep the two atoms at that specific distance, no higher and no lower without experiencing a bias. Since you used UPPER_WALLS before I suggest using it again, except leave off the .max on the argument variable.

UPPER_WALLS ARG= distcn1  AT=2.14 KAPPA=100 EXP=2 OFFSET=0 LABEL=uwall

The above command will not allow the distance between atom 238 and 235 to exceed 2.14 without applying a bias to keep it closer than that. If it appears to not be keeping the atoms at the appropriate distance, try increasing the KAPPA value.

Hope this helps.

Best,

Robert